CellProfiler

CellProfiler is a software designed to analyze images using a reproducible pipeline, adjusting many settings to segment and extract features from images, processing images, and exporting the data to spreadsheet or database [1]. It’s a growing software that accepts contributions and integration with other software with plugins.

Materials

1. How to install CellProfiler with RunCellpose on Windows:

   • video in PT

   • instructions for a Windows machine to install from source in Portuguese or English

Installation

1. To install the executable version of CellProfiler, use their website https://cellprofiler.org/.

2. To install from source on a Mac:

   • For Mac Intel

   • For Mac Apple Silicon

3. To install from source using plugins, follow the instructions here.

Always check the documentation and information available at CellProfiler and CellProfiler/CellProfiler-plugins.

[1] Carpenter, A.E., Jones, T.R., Lamprecht, M.R. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7, R100 (2006). https://doi.org/10.1186/gb-2006-7-10-r100